How can I load data into database using activerecord

I have a ruby script that extracts information from a file (genbank) and I would like to load this data into the database. I have created the model and the schema and a connection script:

require 'active_record'
def establish_connection(db_location= "protein.db.sqlite3")
  ActiveRecord::Base.establish_connection(
    :adapter => "sqlite3",
    :database => db_location,
    :pool => 5,
    :timeout => 5000
  )
end

This is my script that outpu开发者_C百科ts the data:

require 'rubygems'
require 'bio'
require  'snp_db_models'
establish_connection

snp_positions_file = File.open("snp_position.txt")
outfile = File.open("output.txt", "w")
genome_sequence = Bio::FlatFile.open(Bio::EMBL, "ref.embl").next_entry

snp_positions = Array.new
snp_positions_file.gets # header line
while line = snp_positions_file.gets
  snp_details = line.chomp.split("\t")
  snp_seq = snp_details[1]
  snp_positions << snp_details[1].to_i
end


mean_snp_per_base = snp_positions.size/genome_sequence.sequence_length.to_f
puts "Mean snps per base: #{mean_snp_per_base}"

#outfile = File.open("/Volumes/DataRAID/Projects/GAS/fastq_files/bowtie_results/snp_annotation/genes_with_higher_snps.tsv", "w")
outfile.puts("CDS start\tCDS end\tStrand\tGene\tLocus_tag\tnote\tsnp_ID\ttranslation_seq\tProduct\tNo_of_snps_per_gene\tsnp_rate_vs_mean")

genome_sequence.features do |feature|
  if feature.feature !~ /gene/i && feature.feature !~ /source/i 
  start_pos = feature.locations.locations.first.from
  end_pos = feature.locations.locations.first.to

  number_of_snps_in_gene = (snp_positions & (start_pos..end_pos).to_a).size # intersect finds number of times snp occurs within cds location
  mean_snp_per_base_in_gene = number_of_snps_in_gene.to_f/(end_pos - start_pos)

    outfile.print "#{start_pos}\t"
    outfile.print "#{end_pos}\t"
    if feature.locations.locations.first.strand == 1
      outfile.print "forward\t"
    else
      outfile.print "reverse\t"
    end

    qualifiers = feature.to_hash

    ["gene", "locus_tag", "note", "snp_id", "translation", "product"].each do |qualifier|
      if qualifiers.has_key?(qualifier) # if there is gene and product in the file
      #  puts "#{qualifier}: #{qualifiers[qualifier]}"

        outfile.print "#{qualifiers[qualifier].join(",")}\t"
      else
       outfile.print " \t"
      end
    end

    outfile.print "#{number_of_snps_in_gene}\t"
    outfile.print "%.2f" % (mean_snp_per_base_in_gene/mean_snp_per_base)
    outfile.puts
 end
end
outfile.close

How can I load the data in outfile.txt into the database. Do I have to do something like marshall dump?

Thanks in advance

Mark

---

Your can write a rake task to do this. Save it in lib/tasks and give it a .rake extension.

desc "rake task to load data into db"
task :load_data_db  => :environment do
  ...
end

Since the rails environment is loaded, you can access your Model directly as you would in any Rails model/controller. Of course, it'll connect to the database depending on the environment variable defined when you execute your rake task.

---

In a mere script, your models are unknown.

You have to define a minimum to use them as if in a Rails App. Simply declare them:

 class Foo << ActiveRecord:Base

 end

Otherwise, in a Rails context, use rake tasks which are aware of the Rails app details.